The first game I thought of upon reading the title of the article was 'Shadow of the Colossus'. There's a particular boss about half-way through the game who resides in a small secluded garden and the process of defeating them involves tricking them in to ramming over columns etc. until they are trapped.

I have a strong memory of being 12 years old, lying awake at night with the melancholic feeling this article describes, with the realisation that those beasts never did anything to me and I was essentially going out of my way to trick and slaughter them.

No other game has invoked that feeling in me since. It's a very special game. It remains one of my favourites and a stellar example of what the medium can achieve.

The Fallout games often exemplify this: nearly every decision you make is morally ambiguous, and often has far-reaching repercussions in the story and world.

The Cogwork Dancers in Hollow Knight: Silksong are a recent example of this

https://hollowknight.wiki/w/Cogwork_Dancers

For a mainstream boss example I nominate the Lonely Giant in Elder Scrolls Online.

There also are plenty of cute-animal mobs that weren't going to bother you unless you started something. An example that still stands out for me is the first set of sleeping bears in LOTRO.

Another interesting example are hunting games such as Hunter Call of the Wild. I played that for countless hours. While some people simply go for reckless trophy hunting, I thought about most of the shots I took; there's a flock of deer with a single stag, surrounded by does. I knew I would feel awful taking out that single stag, leaving the does behind alone. Could taking it out now be considered "crowd control", how rangers call it? Maybe, under specific circumstances. Or is that just a lie I tell to myself to justify the trophy?

Taking shots on animals living their life in the forest and on the fields imposes a moral/ethical question, especially if you are not being attacked or would otherwise starve to death.

No mention of the Witcher? The whole franchise is based on moral dilemmas like that.